Abstract
Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [¹³C]bicarbonate assimilation assay showed stoichiometric incorporation of ¹³C into Archaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to "Candidatus Nitrosopumilus maritimus" revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N₂O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated "Candidatus Nitrosoarchaeum koreensis."
Publication types
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Ammonia / metabolism*
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Archaea / classification
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Archaea / genetics
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Archaea / isolation & purification*
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Archaea / metabolism*
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Cluster Analysis
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DNA, Archaeal / chemistry
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DNA, Archaeal / genetics
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DNA, Ribosomal / chemistry
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DNA, Ribosomal / genetics
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Genes, rRNA
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Hydrogen-Ion Concentration
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In Situ Hybridization, Fluorescence
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Molecular Sequence Data
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Nitrous Oxide / metabolism
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Oxidation-Reduction
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Oxidoreductases / genetics
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Phylogeny
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RNA, Archaeal / genetics
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RNA, Ribosomal, 16S / genetics
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Sequence Analysis, DNA
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Sequence Homology, Nucleic Acid
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Soil Microbiology*
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Temperature
Substances
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DNA, Archaeal
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DNA, Ribosomal
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RNA, Archaeal
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RNA, Ribosomal, 16S
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Ammonia
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Oxidoreductases
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ammonia monooxygenase
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Nitrous Oxide
Associated data
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GENBANK/HQ331116
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GENBANK/HQ331117
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GENBANK/JF737930
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GENBANK/JF737931
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GENBANK/JF737932
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GENBANK/JF737933
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GENBANK/JF737934
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GENBANK/JF737935
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GENBANK/JF737936
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GENBANK/JF737937
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GENBANK/JF737938
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GENBANK/JF737939
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GENBANK/JF737940
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GENBANK/JF737944
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GENBANK/JF737945
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GENBANK/JF737946
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GENBANK/JF737947
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GENBANK/JF737948
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GENBANK/JF737949
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GENBANK/JF737950
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GENBANK/JF737951
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GENBANK/JF737952
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GENBANK/JF737953
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GENBANK/JF737954
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GENBANK/JF737955
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GENBANK/JF737956
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GENBANK/JF737958
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GENBANK/JF737959
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GENBANK/JF737968
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GENBANK/JF737969